LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
  using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles

units		lj
atom_style	sphere
dimension	2

lattice		sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region		box block 0 60 0 60 -0.5 0.5
create_box	2 box
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 3600 atoms
  create_atoms CPU = 0.001 seconds
change_box      all triclinic
Changing box ...
  triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)

# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms  region sphere1
Deleted 154 atoms, new total = 3446
delete_atoms  region sphere2
Deleted 158 atoms, new total = 3288
create_atoms 2 single 20.0 20.0 0.0 units box
Created 1 atoms
  create_atoms CPU = 0.000 seconds
create_atoms 2 single 60.0 60.0 0.0 units box
Created 1 atoms
  create_atoms CPU = 0.000 seconds

set		type 2 mass 400
Setting atom values ...
  2 settings made for mass
set		type 1 mass 1
Setting atom values ...
  3288 settings made for mass
set     type 2 diameter 20
Setting atom values ...
  2 settings made for diameter
set     type 1 diameter 1
Setting atom values ...
  3288 settings made for diameter

velocity	all create 1.44 87287 loop geom

# multi neighbor and comm for efficiency

neighbor	1 multi/old #multi
neigh_modify	delay 0 #collection/interval 2 1 20
comm_modify     mode multi/old vel yes #reduce/multi

# colloid potential

pair_style      granular
pair_coeff      * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity

fix		1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix		2 all enforce2d
fix             3 all deform 1 xy erate 1e-3

#dump		1 all custom 1000 dump.granular id x y z radius

#dump		2 all image 1000 image.*.jpg type type #		zoom 1.5 center d 0.5 0.5 0.5
#dump_modify	2 pad 5 adiam 1 5.0 adiam 2 1.5

#dump		3 all movie 1000 movie.mpg type type #		zoom 1.5 center d 0.5 0.5 0.5
#dump_modify	3 pad 5 adiam 1 5.0 adiam 2 1.5

thermo_style	custom step temp epair etotal press vol
thermo		1000

timestep	0.005

run		50000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 21
  ghost atom cutoff = 21
  binsize = 1, bins = 85 85 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair granular, perpetual
      attributes: half, newton on, size, history
      pair build: half/size/multi/old/newton/tri
      stencil: half/multi/old/2d/tri
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes
Step Temp E_pair TotEng Press Volume 
       0         1.44            0    1.4395623   0.66837658         7200 
    1000   0.32273428            0   0.32263619   0.17174972    7859.8897 
    2000   0.12441598            0   0.12437817  0.067078155    8212.9946 
    3000  0.067389284            0  0.067368801  0.040425551    8336.7112 
    4000  0.044312733            0  0.044299264  0.028220228    8229.0658 
    5000  0.032702163            0  0.032692223  0.024302012    7931.1298 
    6000     0.025856            0  0.025848141  0.021241317    7603.5534 
    7000  0.021437473            0  0.021430957  0.019285494    7243.5757 
    8000  0.018129567            0  0.018124057  0.020738727    6877.4816 
    9000  0.016370159            0  0.016365184  0.020261904    6515.3445 
   10000   0.01500918            0  0.015004618  0.020551803    6160.4475 
   11000  0.014156551            0  0.014152248  0.021324815    5815.4665 
   12000  0.013725406            0  0.013721235  0.021159958    5483.6304 
   13000  0.013215746            0  0.013211729  0.021685712    5165.4758 
   14000  0.012398153            0  0.012394384  0.024155434    4862.8657 
   15000  0.011842796            0  0.011839196  0.028503991    4577.9008 
   16000  0.011433182            0  0.011429706  0.033564839    4309.8792 
   17000  0.011166574            0   0.01116318  0.040592677    4058.9964 
   18000   0.01100067            0  0.010997326   0.04899206     3825.155 
   19000  0.010224474            0  0.010221366  0.063670337    3607.6577 
   20000 0.0091360558            0 0.0091332789  0.088230111    3408.5658 
   21000 0.0077336471            0 0.0077312964   0.11769368    3227.7002 
   22000 0.0060202357            0 0.0060184059   0.15272492    3064.3986 
   23000 0.0046705738            0 0.0046691542   0.19450723    2918.0014 
   24000 0.0040248311            0 0.0040236078   0.24161743    2788.4113 
   25000 0.0032075267            0 0.0032065518   0.28976925    2674.5604 
   26000 0.0021358008            0 0.0021351516   0.33635615    2574.9564 
   27000 0.0016902771            0 0.0016897633   0.37624261    2487.2379 
   28000 0.0014038216            0 0.0014033949   0.41492061    2409.2461 
   29000 0.00090262588            0 0.00090235152   0.45392924    2340.0308 
   30000 0.00049466445            0 0.0004945141   0.49295063    2279.2316 
   31000 0.00056998139            0 0.00056980814   0.53299532    2226.5683 
   32000 0.00057327032            0 0.00057309607   0.56856551    2181.7093 
   33000 0.00044845449            0 0.00044831818   0.59623461    2142.7574 
   34000 0.00059840346            0 0.00059822157   0.61758978    2107.1254 
   35000 0.00075311121            0 0.0007528823   0.63756791    2072.7217 
   36000 0.00053773653            0 0.00053757309   0.66026022    2039.1654 
   37000 0.00030439696            0 0.00030430444   0.69059127    2007.7901 
   38000 0.00034435616            0 0.00034425149   0.72166346    1980.7136 
   39000 0.00039692535            0 0.0003968047    0.7468036    1957.9531 
   40000 0.0003542502            0 0.00035414252   0.76604173    1937.3834 
   41000 0.0003094667            0 0.00030937263   0.78323183    1916.7027 
   42000 0.00027258976            0 0.0002725069   0.80315572    1895.0714 
   43000 0.00020659987            0 0.00020653707   0.82746098    1873.5408 
   44000 0.00016023865            0 0.00016018994   0.85418945    1853.8677 
   45000 0.00016112731            0 0.00016107833   0.87913874    1837.1144 
   46000 0.00016131366            0 0.00016126463   0.89921653    1822.7355 
   47000 0.00015754747            0 0.00015749958   0.91653641    1809.0285 
   48000 0.00017794764            0 0.00017789356   0.93582953    1794.7043 
   49000 0.00018879338            0  0.000188736   0.95775166    1780.0323 
   50000 0.00017781117            0 0.00017775712   0.97893641    1765.9442 
Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms

Performance: 289297.713 tau/day, 669.671 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 56.696     | 56.696     | 56.696     |   0.0 | 75.93
Neigh   | 2.2232     | 2.2232     | 2.2232     |   0.0 |  2.98
Comm    | 6.1867     | 6.1867     | 6.1867     |   0.0 |  8.29
Output  | 0.0012016  | 0.0012016  | 0.0012016  |   0.0 |  0.00
Modify  | 8.432      | 8.432      | 8.432      |   0.0 | 11.29
Other   |            | 1.125      |            |       |  1.51

Nlocal:        3290.00 ave        3290 max        3290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6295.00 ave        6295 max        6295 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        53729.0 ave       53729 max       53729 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 53729
Ave neighs/atom = 16.331003
Neighbor list builds = 348
Dangerous builds = 0

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:01:14
